train error

[musaxisuoke]

hi
I encountered an error during my training. Can you tell me what might be the reason? This issue has been bothering me for a whole day.

python -m decode.neuralfitter.train.live_engine -p

/data/YX/Decode/test/experimental_data_workflow/beads/Pos0_beads_Z_1/DECODE_train_Pos0_beads_Z_1_MMStack_Default.ome_sml.yaml
Model instantiated.
Model initialised as specified in the constructor.
Sampled dataset in 0.47s. 250284 emitters on 10001 frames.
Sampled dataset in 0.02s. 12743 emitters on 513 frames.
/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/torch/functional.py:504: UserWarning: torch.meshgrid: in an upcoming release, it will be required to pass the indexing argument. (Triggered internally at ../aten/src/ATen/native/TensorShape.cpp:3483.)
return _VF.meshgrid(tensors, **kwargs) # type: ignore[attr-defined]
0%| | 0/8 [00:00<?, ?it/s]/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/decode/neuralfitter/utils/dataloader_customs.py:23: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly. To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
storage = elem.storage()._new_shared(numel)
/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/decode/neuralfitter/utils/dataloader_customs.py:23: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly. To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
storage = elem.storage()._new_shared(numel)
/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/decode/neuralfitter/utils/dataloader_customs.py:23: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly. To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
storage = elem.storage()._new_shared(numel)
/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/decode/neuralfitter/utils/dataloader_customs.py:23: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly. To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
storage = elem.storage()._new_shared(numel)
0%| | 0/8 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/home/peng/miniconda3/envs/decode_env/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/home/peng/miniconda3/envs/decode_env/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/decode/neuralfitter/train/live_engine.py", line 491, in
live_engine_setup(args.param_file, args.device, args.debug, args.no_log,
File "/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/decode/neuralfitter/train/live_engine.py", line 216, in live_engine_setup
val_loss, test_out = decode.neuralfitter.train_val_impl.test(
File "/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/decode/neuralfitter/train_val_impl.py", line 91, in test
loss_val = loss(y_out, y_tar, weight)
File "/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/decode/neuralfitter/loss.py", line 22, in call
return self.forward(output, target, weight)
File "/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/decode/neuralfitter/loss.py", line 271, in forward
gmm_loss = self._compute_gmm_loss(p, pxyz_mu, pxyz_sig, tar_param, tar_mask)
File "/home/peng/miniconda3/envs/decode_env/lib/python3.8/site-packages/decode/neuralfitter/loss.py", line 222, in _compute_gmm_loss
pxyz_mu[:, 1] += self._offset2coord.bin_ctr_x[p_inds[1]].to(pxyz_mu.device)
RuntimeError: indices should be either on cpu or on the same device as the indexed tensor (cpu)

[nolan1999]

Hello,
to see if I can reproduce the issue, can you please specify how you installed Decode? Did you install it via Conda, or clone the repository?
Additionally, how does the "Hardware" section in your parameter file (/data/YX/Decode/test/experimental_data_workflow/beads/Pos0_beads_Z_1/DECODE_train_Pos0_beads_Z_1_MMStack_Default.ome_sml.yaml) look like?

[nolan1999]

Could you please also post the details about your conda environment, i.e. conda activate decode_env; conda list from your terminal?

[musaxisuoke]

Thanks

packages in environment at /home/peng/miniconda3/envs/decode_env:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
absl-py 1.4.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.8.5 py38h01eb140_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.8 h166bdaf_0 conda-forge
anyio 3.7.1 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h27087fc_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py38h0a891b7_3 conda-forge
arrow 1.2.3 pyhd8ed1ab_0 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
babel 2.12.1 pyhd8ed1ab_1 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
blas 2.116 mkl conda-forge
blas-devel 3.9.0 16_linux64_mkl conda-forge
bleach 6.0.0 pyhd8ed1ab_0 conda-forge
blinker 1.6.2 pyhd8ed1ab_0 conda-forge
blosc 1.21.4 h0f2a231_0 conda-forge
brotli 1.0.9 h166bdaf_9 conda-forge
brotli-bin 1.0.9 h166bdaf_9 conda-forge
brotlipy 0.7.0 py38h0a891b7_1005 conda-forge
brunsli 0.1 h9c3ff4c_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.19.1 hd590300_0 conda-forge
c-blosc2 2.10.0 hb4ffafa_0 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.1 pyhd8ed1ab_0 conda-forge
certifi 2023.7.22 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py38h4a40e3a_3 conda-forge
cfitsio 4.1.0 hd9d235c_0 conda-forge
charls 2.3.4 h9c3ff4c_0 conda-forge
charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge
click 8.1.6 unix_pyh707e725_0 conda-forge
cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge
cmake 3.27.0 pypi_0 pypi
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.1.3 pyhd8ed1ab_0 conda-forge
cryptography 41.0.2 py38hcdda232_0 conda-forge
cudatoolkit 11.8.0 h4ba93d1_12 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cytoolz 0.12.2 py38h01eb140_0 conda-forge
dask-core 2023.5.0 pyhd8ed1ab_0 conda-forge
dav1d 1.0.0 h166bdaf_1 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.6.7 py38h8dc9893_0 conda-forge
decode 0.10.2 np119py_0 turagalab
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.14 pyh1a96a4e_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.1.2 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fftw 3.3.10 nompi_hc118613_108 conda-forge
filelock 3.12.2 pypi_0 pypi
flit-core 3.9.0 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.41.1 py38h01eb140_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
frozenlist 1.4.0 py38h01eb140_0 conda-forge
fsspec 2023.6.0 pyh1a96a4e_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
gitdb 4.0.10 pyhd8ed1ab_0 conda-forge
gitpython 3.1.32 pyhd8ed1ab_0 conda-forge
glib 2.76.4 hfc55251_0 conda-forge
glib-tools 2.76.4 hfc55251_0 conda-forge
google-auth 2.22.0 pyh1a96a4e_0 conda-forge
google-auth-oauthlib 1.0.0 pyhd8ed1ab_1 conda-forge
grpcio 1.56.2 py38h94a1851_0 conda-forge
gst-plugins-base 1.21.3 h4243ec0_1 conda-forge
gstreamer 1.21.3 h25f0c4b_1 conda-forge
gstreamer-orc 0.4.34 hd590300_0 conda-forge
h5py 3.7.0 nompi_py38h045baee_101 conda-forge
hdf5 1.12.2 nompi_h4df4325_101 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
imagecodecs 2022.8.8 py38hf09e3b1_5 conda-forge
imageio 2.31.1 pyh24c5eb1_0 conda-forge
importlib-metadata 6.8.0 pyha770c72_0 conda-forge
importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge
importlib_resources 6.0.0 pyhd8ed1ab_1 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.25.0 pyh71e2992_0 conda-forge
ipython 8.12.2 pyh41d4057_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jack 1.9.22 h11f4161_0 conda-forge
jedi 0.18.2 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.3.0 pyhd8ed1ab_1 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsonpointer 2.0 py_0 conda-forge
jsonschema 4.18.4 pyhd8ed1ab_0 conda-forge
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jsonschema-with-format-nongpl 4.18.4 pyhd8ed1ab_0 conda-forge
jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge
jupyter_client 8.3.0 pyhd8ed1ab_0 conda-forge
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jupyter_events 0.7.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.7.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyterlab 4.0.3 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.24.0 pyhd8ed1ab_0 conda-forge
jxrlib 1.1 h7f98852_2 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py38h43d8883_1 conda-forge
krb5 1.20.1 h81ceb04_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.14 h6ed2654_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20230125.3 cxx17_h59595ed_0 conda-forge
libaec 1.0.6 hcb278e6_1 conda-forge
libavif 0.10.1 h5cdd6b5_2 conda-forge
libblas 3.9.0 16_linux64_mkl conda-forge
libbrotlicommon 1.0.9 h166bdaf_9 conda-forge
libbrotlidec 1.0.9 h166bdaf_9 conda-forge
libbrotlienc 1.0.9 h166bdaf_9 conda-forge
libcap 2.67 he9d0100_0 conda-forge
libcblas 3.9.0 16_linux64_mkl conda-forge
libclang 15.0.7 default_h7634d5b_3 conda-forge
libclang13 15.0.7 default_h9986a30_3 conda-forge
libcups 2.3.3 h36d4200_3 conda-forge
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libdb 6.2.32 h9c3ff4c_0 conda-forge
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libpq 15.3 hbcd7760_1 conda-forge
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libsndfile 1.2.0 hb75c966_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
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lit 16.0.6 pypi_0 pypi
llvm-openmp 16.0.6 h4dfa4b3_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
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oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge
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pip 23.2.1 pyhd8ed1ab_0 conda-forge
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ply 3.11 py_1 conda-forge
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protobuf 4.23.3 py38h830738e_0 conda-forge
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python 3.8.17 he550d4f_0_cpython conda-forge
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python-fastjsonschema 2.18.0 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python_abi 3.8 3_cp38 conda-forge
pytorch-mutex 1.0 cpu pytorch
pytz 2023.3 pyhd8ed1ab_0 conda-forge
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pywavelets 1.3.0 py38h71d37f0_1 conda-forge
pyyaml 6.0 py38h0a891b7_5 conda-forge
pyzmq 25.1.0 py38h509eb50_0 conda-forge
qt-main 5.15.6 hf6cd601_5 conda-forge
re2 2023.03.02 h8c504da_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.30.0 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rpds-py 0.9.2 py38h0cc4f7c_0 conda-forge
rsa 4.9 pyhd8ed1ab_0 conda-forge
scikit-image 0.19.3 py38h47df419_1 conda-forge
scikit-learn 1.1.2 py38h0b08f9b_0 conda-forge
scipy 1.8.0 py38h56a6a73_1 conda-forge
seaborn 0.10.1 1 conda-forge
seaborn-base 0.10.1 py_1 conda-forge
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setuptools 68.0.0 pyhd8ed1ab_0 conda-forge
sip 6.7.10 py38h17151c0_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 3.0.5 pyh44b312d_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
spline 0.10.0 np119py38heb0550a_1 turagalab
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.13.2 py38h71d37f0_0 conda-forge
sympy 1.12 pypi_0 pypi
tbb 2021.9.0 hf52228f_0 conda-forge
tensorboard 2.13.0 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.7.0 py38h3d167d9_0 conda-forge
terminado 0.17.1 pyh41d4057_0 conda-forge
threadpoolctl 3.2.0 pyha21a80b_0 conda-forge
tifffile 2022.4.8 pyhd8ed1ab_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
torch 2.0.1 pypi_0 pypi
torchaudio 2.0.2 pypi_0 pypi
torchvision 0.15.2 pypi_0 pypi
tornado 6.3.2 py38h01eb140_0 conda-forge
tqdm 4.65.0 pyhd8ed1ab_1 conda-forge
traitlets 5.9.0 pyhd8ed1ab_0 conda-forge
triton 2.0.0 pypi_0 pypi
typing-extensions 4.7.1 hd8ed1ab_0 conda-forge
typing_extensions 4.7.1 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
unicodedata2 15.0.0 py38h0a891b7_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 1.26.15 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.6.1 pyhd8ed1ab_0 conda-forge
werkzeug 2.3.6 pyhd8ed1ab_0 conda-forge
wheel 0.41.0 pyhd8ed1ab_0 conda-forge
wrapt 1.15.0 py38h1de0b5d_0 conda-forge
xcb-util 0.4.0 h166bdaf_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h166bdaf_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h166bdaf_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.2 py38h01eb140_0 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zfp 1.0.0 h27087fc_3 conda-forge
zipp 3.16.2 pyhd8ed1ab_0 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstd 1.5.2 hfc55251_7 conda-forge

[nolan1999]

Thank you.
I could reproduce the problem using the same environment as yours. This does not happen when creating the environment as detailed in https://decode.readthedocs.io/en/release-0.10/installation.html#installation-in-terminal-macos-linux-anaconda-prompt-on-windows, at least on my machine. Have you used the command written there to create the environment (remember to use the right conda create command based on the platform you are working on)? The torch library should not come from the pypi channel in that case.
If this does not work: Are you on Mac, Linux, or Windows? Do you have a gpu on your machine?

[musaxisuoke]

I found that the error was caused by installing cuda11.8. After downgrading the cuda version to 11.3, it can run normally now. Thank you for your help these days.